Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Nr3c1

Cell type

Cell type Class
Liver
Cell type
Hepatocytes
MeSH Description
The main structural component of the LIVER. They are specialized EPITHELIAL CELLS that are organized into interconnected plates called lobules.

Attributes by original data submitter

Sample

source_name
hepatocytes
tissue
liver
strain
C57BL/6JOlaHsd
antibody
GR (Cell Signaling Technologies cat# 3660)
cell type
hepatocytes

Sequenced DNA Library

library_name
GSM5696914
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA: Total RNA was isolated from primary mouse hepatocytes using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer's protocol. ChIP: cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125M glycine. Crosslinked samples were washed in PBS, resuspended in ChIP lysis buffer (0.5% SDS, 10mM EDTA, 50mM Tris-HCl pH8) and sonicated (Bioruptor, Diagenode) to release 100-1000 bp fragments. Antibodies (4 μg per 300 μg chromatin) against H3K27ac (Active motif #39133) or GR (CST #3660) were conjugated to magnetic beads (Sera-Mag, Merck #GE17152104010150) for 2 h at 4°C. Chromatin was immunoprecipitated with antibody-bead conjugates over night at 4°C. Immunocomplexes were washed sequentially with the following buffers: low-salt buffer (0.01% SDS, 1% Triton x-100, 2 mM EDTA, 20mM Tris-HCl pH8, 150mM NaCl), high salt buffer (0.01% SDS, 1% Triton x-100, 2mM EDTA, 20mM Tris-HCl pH8, 500mM NaCl), low salt buffer and TE buffer (10mMTris-HCl, 1mM EDTA pH8). Chromatin was de-proteinized with proteinase K (Hy Labs EPR9016) for 2 h at 55°C and de-crosslinked over night at 65°C. DNA was subsequently phenol-chloroform purified and ethanol precipitated For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ChIP DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
36053368
Reads aligned (%)
92.8
Duplicates removed (%)
23.5
Number of peaks
483 (qval < 1E-05)

mm9

Number of total reads
36053368
Reads aligned (%)
92.5
Duplicates removed (%)
23.5
Number of peaks
469 (qval < 1E-05)

Base call quality data from DBCLS SRA